def Step3(self):
""" Step3()
Process graph to remove unwanted edges.
"""
# Check if we can go
if self._vol is None or self._params is None:
raise ValueError('Data or params not yet given.')
if self._nodes2 is None:
raise ValueError('Edges not yet calculated.')
# Get nodes and params
#nodes = stentgraph.StentGraph()
#nodes.unpack( self._nodes2.pack() )
nodes = self._nodes2.copy()
params = self._params
# Init times
t_start = time.time()
t_clean = 0
print('Step3 in StentDirect_test is indeed used :)')
# Iteratively prune the graph. The order of operations should
# not matter too much, although in practice there is a
# difference. In particular the prune_weak and prune_redundant
# have a similar function and should be executed in this order.
cur_edges = 0
count = 0
while cur_edges != nodes.number_of_edges():
count += 1
cur_edges = nodes.number_of_edges()
ene = params.graph_expectedNumberOfEdges
stentgraph.prune_very_weak(nodes, params.graph_weakThreshold)
stentgraph.prune_weak(nodes, ene, params.graph_strongThreshold)
stentgraph.prune_redundant(nodes, params.graph_strongThreshold)
stentgraph.prune_clusters(nodes, params.graph_minimumClusterSize)
stentgraph.prune_tails(nodes, params.graph_trimLength)
stentgraph.pop_nodes(nodes)
stentgraph.add_corner_nodes(nodes)
stentgraph.smooth_paths(nodes)
t0 = time.time() - t_start
tmp = "Reduced to %i edges, "
tmp += "which took %1.2f s (%i iters)"
print(tmp % (nodes.number_of_edges(), t0, count))
print("****************************************")
# Finish
self._nodes3 = nodes
if self._draw:
self.Draw(3)
return nodes
def get_midpoints_peaksvalleys(model):
""" Get midpoints near the peaks and valleys
"""
# remove hooks, pop nodes
model_hooks1, model_noHooks1 = _get_model_hooks(model)
stentgraph.pop_nodes(model_noHooks1)
midpoints_peaks_valleys = PointSet(3)
for n1, n2 in sorted(model_noHooks1.edges()):
if stentgraph._edge_length(model_noHooks1, n1, n2) < 10: # in mm
# get midpoint for edges near struts
mid = (n1[0] + n2[0]) / 2, (n1[1] + n2[1]) / 2, (n1[2] + n2[2]) / 2
path = model_noHooks1.edge[n1][n2]['path']
mid_and_pathpoint = point_in_pointcloud_closest_to_p(path, mid)
midpoints_peaks_valleys.append(
mid_and_pathpoint[0]) # append pp_point
return midpoints_peaks_valleys
def test_pop_nodes(self):
# Create dummy paths
path1 = PointSet(2)
path1.append(1, 11)
path1.append(1, 12)
# create 4 nodes (6-7-8-9), remove 8
graph = StentGraph()
graph.add_edge(6, 7, cost=4, ctvalue=70, path=path1)
graph.add_edge(7, 8, cost=2, ctvalue=50, path=path1)
graph.add_edge(8, 9, cost=3, ctvalue=60, path=path1)
graph0 = graph.copy()
# Pop straight line
graph = graph0.copy()
pop_nodes(graph)
assert graph.number_of_nodes() == 2
assert graph.number_of_edges() == 1
assert graph.edge[6][9]['path'].shape[0] == 3 + 1
# Pop cycle
graph = graph0.copy()
graph.add_edge(9, 6, cost=3, ctvalue=60, path=path1)
pop_nodes(graph)
assert graph.number_of_nodes() == 1
assert graph.number_of_edges() == 1
n = graph.nodes()[0]
assert graph.edge[n][n]['path'].shape[0] == 4 + 1 + 1 # cycle
# arbitrary what node stayed around
# Pop with one side branch popping
graph = graph0.copy()
graph.add_edge(7, 2, cost=3, ctvalue=60, path=path1)
pop_nodes(graph)
assert graph.number_of_nodes() == 4
assert graph.number_of_edges() == 3
assert graph.edge[7][9]['path'].shape[0] == 2 + 1
# Pop with one prevent popping
graph = graph0.copy()
graph.node[7]['nopop'] = True
pop_nodes(graph)
assert graph.number_of_nodes() == 3
assert graph.number_of_edges() == 2
assert graph.edge[7][9]['path'].shape[0] == 2 + 1
def on_key(event):
"""KEY commands for user interaction
'UP/DOWN = show/hide nodes'
'DELETE = remove edge [select 2 nodes] or pop node [select 1 node] '
'or remove seed in nodes1 closest to [picked point]'
'p = remove seeds posterior (y-axis) to [picked point] (use for spine seeds)'
'o = remove seeds anterior (y-axis) to [picked point]'
'i = remove seeds proximal (z-axis) to [picked point]'
'k = remove seeds distal (z-axis) to [picked point]'
'l = remove seeds left (x-axis) to [picked point]'
'j = remove seeds right (x-axis) to [picked point]'
'ALT = clean graph: remove residual clusters, pop, corner'
'PageUp= protect node closest to picked point in nodes1 axes, no pop
'n = add [picked point] (SHIFT+R-click) as seed'
'1 = redo step 1; 2 = redo step 2; 3 = redo step 3'
'z/x/a/d = axis invisible/visible/rotate'
"""
global label
global node_points
global sd
if event.key == vv.KEY_DOWN:
# hide nodes
t1.visible = False
t2.visible = False
t3.visible = False
if 'node_points' in globals():
for node_point in node_points:
node_point.visible = False
if event.key == vv.KEY_UP:
# show nodes
if 'node_points' in globals():
for node_point in node_points:
node_point.visible = True
if event.key == vv.KEY_DELETE:
if len(selected_nodes) == 0:
# remove node closest to picked point
node = _utils_GUI.snap_picked_point_to_graph(sd._nodes1, vol, label, nodesOnly=True)
sd._nodes1.remove_node(node)
view = a1.GetView()
a1.Clear()
label = DrawModelAxes(vol, sd._nodes1, a1, clim=clim, showVol=showVol, removeStent=False)
a1.SetView(view)
if len(selected_nodes) == 2:
# remove edge
select1 = selected_nodes[0].node
select2 = selected_nodes[1].node
c = sd._nodes3.edge[select1][select2]['cost']
ct = sd._nodes3.edge[select1][select2]['ctvalue']
path = sd._nodes3.edge[select1][select2]['path']
l = stentgraph._edge_length(sd._nodes3, select1, select2)
sd._nodes3.remove_edge(select1, select2)
stentgraph.pop_nodes(sd._nodes3) # pop residual nodes
# Visualize removed edge, show keys and deselect nodes
selected_nodes[1].faceColor = 'b'
selected_nodes[0].faceColor = 'b'
selected_nodes.clear()
t1.text = 'Edge ctvalue: \b{%1.2f HU}' % ct
t2.text = 'Edge cost: \b{%1.7f }' % c
t3.text = 'Edge length: \b{%1.2f mm}' % l
t1.visible = True
t2.visible = True
t3.visible = True
view = a3.GetView()
pp = Pointset(path)
line = vv.solidLine(pp, radius = 0.2)
line.faceColor = 'r'
a3.SetView(view)
if len(selected_nodes) == 1:
# pop node
select1 = selected_nodes[0].node
stentgraph._pop_node(sd._nodes3, select1) # asserts degree == 2
selected_nodes[0].faceColor = 'w'
selected_nodes.clear()
if event.key == vv.KEY_ALT:
# ALT will FINISH model
stentgraph.prune_clusters(sd._nodes3, 3) #remove residual nodes/clusters
stentgraph.pop_nodes(sd._nodes3)
stentgraph.add_corner_nodes(sd._nodes3, th=sd._params.graph_angleVector, angTh=sd._params.graph_angleTh)
# Create mesh and visualize
view = a3.GetView()
a3.Clear()
DrawModelAxes(vol, sd._nodes3, a3, meshColor=meshColor, clim=clim, showVol=showVol, lc='g', mw=8, lw=0.2)
# _utils_GUI.vis_spared_edges(sd._nodes3)
a3.SetView(view)
print('----DO NOT FORGET TO SAVE THE MODEL TO DISK; RUN _SAVE_SEGMENTATION----')
if event.text == 'n':
# add picked seed to nodes_1
coord2 = get_picked_seed(vol, label)
sd._nodes1.add_node(tuple(coord2))
view = a1.GetView()
point = vv.plot(coord2[0], coord2[1], coord2[2], mc= 'b', ms = 'o', mw= 8, alpha=0.5, axes=a1)
a1.SetView(view)
if event.key == vv.KEY_PAGEUP:
# protect node from pop
pickedNode = _utils_GUI.snap_picked_point_to_graph(sd._nodes1, vol, label, nodesOnly=True)
sd._nodes1.add_node(pickedNode, nopop = True)
sd._nodes2.add_node(pickedNode, nopop = True)
view = a1.GetView()
point = vv.plot(pickedNode[0], pickedNode[1], pickedNode[2], mc= 'y', ms = 'o', mw= 8, alpha=0.5, axes=a1)
a1.SetView(view)
# now rerun step 3
if event.text == 'p':
# remove false seeds posterior to picked point, e.g. for spine
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2, vol, a2, label,
clim, location='posterior', showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1, vol, a1, label,
clim, location='posterior', showVol=showVol)
if event.text == 'o':
# remove seeds prox to selected point
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2, vol, a1, label,
clim, location='anterior', showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1, vol, a1, label,
clim, location='anterior', showVol=showVol)
if event.text == 'i':
# remove seeds prox to selected point
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2, vol, a1, label,
clim, location='proximal', showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1, vol, a1, label,
clim, location='proximal', showVol=showVol)
if event.text == 'k':
# remove seeds dist to selected point
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2, vol, a1, label,
clim, location='distal', showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1, vol, a1, label,
clim, location='distal', showVol=showVol)
if event.text == 'l':
# remove seeds left to selected point
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2, vol, a1, label,
clim, location='left', showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1, vol, a1, label,
clim, location='left', showVol=showVol)
if event.text == 'j':
# remove seeds right to selected point
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2, vol, a1, label,
clim, location='right', showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1, vol, a1, label,
clim, location='right', showVol=showVol)
if event.text == '1':
# redo step1
view = a1.GetView()
a1.Clear(); a2.Clear(); a3.Clear()
sd._params = p
sd.Step1()
label = DrawModelAxes(vol, sd._nodes1, a1, clim=clim, showVol=showVol, removeStent=False) # lc, mc
a1.SetView(view)
if event.text == '2':
# redo step2
view = a2.GetView()
a2.Clear(); a3.Clear()
sd._params = p
sd.Step2()
DrawModelAxes(vol, sd._nodes2, a2, clim=clim, showVol=showVol,removeStent=False)
a2.SetView(view)
if event.text == '3':
# redo step3
view = a3.GetView()
a3.Clear()
sd._params = p
sd.Step3(cleanNodes=True)
DrawModelAxes(vol, sd._nodes3, a3, meshColor=meshColor, clim=clim, showVol=showVol,removeStent=False)
node_points = _utils_GUI.interactive_node_points(sd._nodes3, scale=0.6)
_utils_GUI.node_points_callbacks(node_points, selected_nodes, pick=False)
a3.SetView(view)
def on_key(event):
"""KEY commands for user interaction
'UP/DOWN = show/hide nodes'
'DELETE = remove edge [select 2 nodes] or pop node [select 1 node] '
'or remove seed in nodes1 closest to [picked point]'
'PageDown = remove graph posterior (y-axis) to [picked point] (use for spine seeds)'
'ALT = clean graph: remove residual clusters, pop, corner'
'CTRL+SHIFT = add [picked point] (SHIFT+R-click) as seed'
"""
global label
global node_points
global sd
if event.key == vv.KEY_DOWN:
# hide nodes
t1.visible = False
t2.visible = False
t3.visible = False
for node_point in node_points:
node_point.visible = False
if event.key == vv.KEY_UP:
# show nodes
for node_point in node_points:
node_point.visible = True
if event.key == vv.KEY_DELETE:
if len(selected_nodes) == 0:
# remove node closest to picked point
node = _utils_GUI.snap_picked_point_to_graph(sd._nodes1,
vol,
label,
nodesOnly=True)
sd._nodes1.remove_node(node)
view = a1.GetView()
a1.Clear()
label = DrawModelAxes(vol,
sd._nodes1,
a1,
clim=clim,
showVol=showVol,
removeStent=False)
a1.SetView(view)
if len(selected_nodes) == 2:
# remove edge
select1 = selected_nodes[0].node
select2 = selected_nodes[1].node
c = sd._nodes3.edge[select1][select2]['cost']
ct = sd._nodes3.edge[select1][select2]['ctvalue']
path = sd._nodes3.edge[select1][select2]['path']
l = stentgraph._edge_length(sd._nodes3, select1, select2)
sd._nodes3.remove_edge(select1, select2)
stentgraph.pop_nodes(sd._nodes3) # pop residual nodes
# Visualize removed edge, show keys and deselect nodes
selected_nodes[1].faceColor = 'b'
selected_nodes[0].faceColor = 'b'
selected_nodes.clear()
t1.text = 'Edge ctvalue: \b{%1.2f HU}' % ct
t2.text = 'Edge cost: \b{%1.7f }' % c
t3.text = 'Edge length: \b{%1.2f mm}' % l
t1.visible = True
t2.visible = True
t3.visible = True
view = a3.GetView()
pp = Pointset(path)
line = vv.solidLine(pp, radius=0.2)
line.faceColor = 'r'
# a3.SetView(view)
if len(selected_nodes) == 1:
# pop node
select1 = selected_nodes[0].node
stentgraph._pop_node(sd._nodes3, select1) # asserts degree == 2
selected_nodes[0].faceColor = 'w'
selected_nodes.clear()
if event.key == vv.KEY_ALT:
# ALT will FINISH model
stentgraph.prune_clusters(sd._nodes3,
3) #remove residual nodes/clusters
stentgraph.pop_nodes(sd._nodes3)
stentgraph.add_corner_nodes(sd._nodes3,
th=sd._params.graph_angleVector,
angTh=sd._params.graph_angleTh)
# Create mesh and visualize
view = a3.GetView()
a3.Clear()
DrawModelAxes(vol,
sd._nodes3,
a3,
meshColor=meshColor,
clim=clim,
showVol=showVol,
lc='b',
mw=8,
lw=0.2)
_utils_GUI.vis_spared_edges(sd._nodes3)
a3.SetView(view)
print(
'----DO NOT FORGET TO SAVE THE MODEL TO DISK; RUN _SAVE_SEGMENTATION----'
)
if event.text == 'n':
# add picked seed to nodes_1
coord2 = get_picked_seed(vol, label)
sd._nodes1.add_node(tuple(coord2))
view = a1.GetView()
point = vv.plot(coord2[0],
coord2[1],
coord2[2],
mc='b',
ms='o',
mw=8,
alpha=0.5,
axes=a1)
a1.SetView(view)
if event.text == 'p':
# protect node from pop
pickedNode = _utils_GUI.snap_picked_point_to_graph(sd._nodes1,
vol,
label,
nodesOnly=True)
sd._nodes1.add_node(pickedNode, nopop=True)
sd._nodes2.add_node(pickedNode, nopop=True)
view = a1.GetView()
point = vv.plot(pickedNode[0],
pickedNode[1],
pickedNode[2],
mc='y',
ms='o',
mw=8,
alpha=0.5,
axes=a1)
a1.SetView(view)
# now rerun step 3
if event.key == vv.KEY_PAGEDOWN:
# remove false seeds posterior to picked point, e.g. for spine
try:
_utils_GUI.remove_nodes_by_selected_point(sd._nodes3,
vol,
a3,
label,
clim,
showVol=showVol)
except ValueError: # false nodes already cleaned by Step3
pass
_utils_GUI.remove_nodes_by_selected_point(sd._nodes2,
vol,
a2,
label,
clim,
showVol=showVol)
label = _utils_GUI.remove_nodes_by_selected_point(sd._nodes1,
vol,
a1,
label,
clim,
showVol=showVol)
if event.text == '1':
# redo step1
view = a1.GetView()
a1.Clear()
a2.Clear()
a3.Clear()
sd._params = p
sd.Step1()
label = DrawModelAxes(vol,
sd._nodes1,
a1,
clim=clim,
showVol=showVol,
removeStent=False) # lc, mc
a1.SetView(view)
if event.text == '2':
# redo step2 and 3
view = a2.GetView()
a2.Clear()
a3.Clear()
sd._params = p
sd.Step2()
sd.Step3(cleanNodes=cleanNodes)
DrawModelAxes(vol,
sd._nodes2,
a2,
clim=clim,
showVol=showVol,
removeStent=False)
DrawModelAxes(vol,
sd._nodes3,
a3,
meshColor=meshColor,
clim=clim,
showVol=showVol,
removeStent=False)
a2.SetView(view)
if event.text == '3':
view = a3.GetView()
a3.Clear()
sd._params = p
sd.Step3(cleanNodes=cleanNodes)
DrawModelAxes(vol,
sd._nodes3,
a3,
meshColor=meshColor,
clim=clim,
showVol=showVol,
removeStent=False)
node_points = _utils_GUI.interactive_node_points(sd._nodes3, scale=0.6)
_utils_GUI.node_points_callbacks(node_points,
selected_nodes,
pick=False)
a3.SetView(view)
if event.text == 's':
# SAVE SEGMENTATION
# make centerline points of segmentation
paths_as_pp = points_from_edges_in_graph(sd._nodes3, type='order')
ringpoints = paths_as_pp[0].T
# Get graph model
model = sd._nodes3
seeds = sd._nodes1
Draw = sd.Draw
# Build struct
s2 = vv.ssdf.new()
# We do not need croprange, but keep for reference
s2.sampling = s.sampling
s2.origin = s.origin
s2.stenttype = s.stenttype
s2.croprange = s.croprange
for key in dir(s):
if key.startswith('meta'):
suffix = key[4:]
s2['meta' + suffix] = s['meta' + suffix]
s2.what = what
s2.params = p
s2.stentType = stentType
# Store model
s2.model = model.pack()
s2.seeds = seeds.pack()
s2.Draw = Draw
s2.ringpoints = ringpoints
#s2.mesh = ssdf.new()
# Save
savedir = select_dir(
r'C:\Users\Gebruiker\Google Drive\Afstuderen\Rings')
filename = '%s_%s_%s_%s_%s.ssdf' % (ptcode, ctcode, cropname,
'model' + what, ring)
ssdf.save(os.path.join(savedir, filename), s2)
print('saved to disk in {} as {}.'.format(savedir, filename))
def on_key(event):
"""KEY commands for user interaction
UP/DOWN = show/hide nodes
ENTER = restore edge [select 2 nodes]
DELETE = remove edge [select 2 ndoes] or pop node [select 1 node]'
ALT = clean graph: pop, crossings, corner
ESCAPE = FINISH: refine, smooth
"""
global node_points
global nodes3copy
if event.key == vv.KEY_DOWN:
# hide nodes
t1.visible = False
t2.visible = False
t3.visible = False
for node_point in node_points:
node_point.visible = False
if event.key == vv.KEY_UP:
# show nodes
for node_point in node_points:
node_point.visible = True
if event.key == vv.KEY_ENTER:
# restore edge
assert len(selected_nodes) == 2
select1 = selected_nodes[0].node
select2 = selected_nodes[1].node
c = sd._nodes2.edge[select1][select2]['cost']
ct = sd._nodes2.edge[select1][select2]['ctvalue']
p = sd._nodes2.edge[select1][select2]['path']
sd._nodes3.add_edge(select1, select2, cost=c, ctvalue=ct, path=p)
l = stentgraph._edge_length(sd._nodes3, select1, select2)
# Visualize restored edge and deselect nodes
selected_nodes[1].faceColor = 'b'
selected_nodes[0].faceColor = 'b'
selected_nodes.clear()
t1.text = 'Edge ctvalue: \b{%1.2f HU}' % ct
t2.text = 'Edge cost: \b{%1.7f }' % c
t3.text = 'Edge length: \b{%1.2f mm}' % l
t1.visible = True
t2.visible = True
t3.visible = True
view = a3.GetView()
pp = Pointset(p) # visvis meshes do not work with PointSet
line = vv.solidLine(pp, radius=0.2)
line.faceColor = 'g'
a3.SetView(view)
if event.key == vv.KEY_DELETE:
if len(selected_nodes) == 2:
# remove edge
select1 = selected_nodes[0].node
select2 = selected_nodes[1].node
c = sd._nodes3.edge[select1][select2]['cost']
ct = sd._nodes3.edge[select1][select2]['ctvalue']
p = sd._nodes3.edge[select1][select2]['path']
l = stentgraph._edge_length(sd._nodes3, select1, select2)
sd._nodes3.remove_edge(select1, select2)
# visualize removed edge, show keys and deselect nodes
selected_nodes[1].faceColor = 'b'
selected_nodes[0].faceColor = 'b'
selected_nodes.clear()
t1.text = 'Edge ctvalue: \b{%1.2f HU}' % ct
t2.text = 'Edge cost: \b{%1.7f }' % c
t3.text = 'Edge length: \b{%1.2f mm}' % l
t1.visible = True
t2.visible = True
t3.visible = True
view = a3.GetView()
pp = Pointset(p)
line = vv.solidLine(pp, radius=0.2)
line.faceColor = 'r'
a3.SetView(view)
if len(selected_nodes) == 1:
# pop node
select1 = selected_nodes[0].node
stentgraph._pop_node(sd._nodes3, select1) # asserts degree == 2
selected_nodes[0].faceColor = 'w'
selected_nodes.clear()
if event.key == vv.KEY_ALT:
#backup to restore
nodes3copy = sd._nodes3.copy()
# clean nodes
if stentType == 'anacondaRing':
stentgraph.add_nodes_at_crossings(sd._nodes3)
stentgraph.pop_nodes(
sd._nodes3) # pop before corner detect or angles can not be found
stentgraph.add_corner_nodes(sd._nodes3,
th=sd._params.graph_angleVector,
angTh=sd._params.graph_angleTh)
stentgraph.pop_nodes(
sd._nodes3
) # because removing edges/add nodes can create degree 2 nodes
stentgraph.prune_tails(sd._nodes3, sd._params.graph_trimLength)
stentgraph.prune_clusters(sd._nodes3,
3) #remove residual nodes/clusters
# visualize result
view = a3.GetView()
a3.Clear()
DrawModelAxes(vol,
sd._nodes3,
a3,
clim=clim,
showVol=showVol,
mw=8,
lw=0.2,
climEditor=False)
node_points = _utils_GUI.interactive_node_points(sd._nodes3, scale=0.6)
_utils_GUI.node_points_callbacks(node_points,
selected_nodes,
pick=False)
a3.SetView(view)
print('----Press ESCAPE to FINISH model----')
if event.text == 'u':
# undo and restore nodes3
sd._nodes3 = nodes3copy
view = a3.GetView()
a3.Clear()
DrawModelAxes(vol,
sd._nodes3,
a3,
clim=clim,
showVol=showVol,
mw=8,
lw=0.2,
climEditor=False)
node_points = _utils_GUI.interactive_node_points(sd._nodes3, scale=0.6)
_utils_GUI.node_points_callbacks(node_points,
selected_nodes,
pick=False)
a3.SetView(view)
if event.key == vv.KEY_ESCAPE:
#backup to restore
nodes3copy = sd._nodes3.copy()
# ESCAPE will FINISH model
stentgraph.pop_nodes(sd._nodes3)
sd._nodes3 = sd._RefinePositions(sd._nodes3) # subpixel locations
stentgraph.smooth_paths(sd._nodes3, 4)
# Create mesh and visualize
view = a3.GetView()
a3.Clear()
DrawModelAxes(vol,
sd._nodes3,
a3,
meshColor='g',
clim=clim,
showVol=showVol,
lc='w',
mw=8,
lw=0.2,
climEditor=False)
node_points = _utils_GUI.interactive_node_points(sd._nodes3, scale=0.6)
_utils_GUI.node_points_callbacks(node_points,
selected_nodes,
pick=False)
a3.SetView(view)
print(
'----DO NOT FORGET TO SAVE THE MODEL TO DISK; RUN _SAVE_SEGMENTATION----'
)
if event.text == 'r':
# restore this node
pickedNode = _utils_GUI.snap_picked_point_to_graph(
sd._nodes2, vol, label, nodesOnly=True) # x,y,z
sd._nodes3.add_node(pickedNode)
view = a3.GetView()
a3.Clear()
DrawModelAxes(vol,
sd._nodes3,
a3,
clim=clim,
showVol=showVol,
mw=8,
lw=0.2,
climEditor=False)
node_points = _utils_GUI.interactive_node_points(sd._nodes3, scale=0.6)
_utils_GUI.node_points_callbacks(node_points,
selected_nodes,
pick=False)
a3.SetView(view)
if event.text == 's':
# additional smooth
stentgraph.smooth_paths(sd._nodes3, 2)
view = a3.GetView()
a3.Clear()
DrawModelAxes(vol,
sd._nodes3,
a3,
clim=clim,
showVol=showVol,
mw=8,
lw=0.2,
climEditor=False)
node_points = _utils_GUI.interactive_node_points(sd._nodes3, scale=0.6)
_utils_GUI.node_points_callbacks(node_points,
selected_nodes,
pick=False)
a3.SetView(view)
if event.text == 'e':
# smooth selected edge
edgegraph = stentgraph.StentGraph() #empty graph
select1 = selected_nodes[0].node
select2 = selected_nodes[1].node
edge_info = sd._nodes3.edge[select1][select2]
edgegraph.add_edge(select1, select2, **edge_info)
stentgraph.smooth_paths(edgegraph, 4)
sd._nodes3.edge[select1][select2]['path'] = edgegraph.edge[select1][
select2]['path']
view = a3.GetView()
a3.Clear()
DrawModelAxes(vol,
sd._nodes3,
a3,
clim=clim,
showVol=showVol,
mw=8,
lw=0.2,
climEditor=False)
node_points = _utils_GUI.interactive_node_points(sd._nodes3, scale=0.6)
_utils_GUI.node_points_callbacks(node_points,
selected_nodes,
pick=False)
# see if node_points are still selected to color them red
for node_point in node_points:
node_point.visible = True
for i, node in enumerate(selected_nodes):
if node_point.node == node.node:
selected_nodes[i] = node_point
node_point.faceColor = (1, 0, 0)
a3.SetView(view)
if event.text == 'w':
for n in selected_nodes:
n.faceColor = 'b'
selected_nodes.clear()
if event.text == 'q':
view = a3.GetView()
_utils_GUI.interactiveClusterRemoval(sd._nodes3)
a3.SetView(view)
model_hooks = stentgraph.StentGraph()
remove = True
hooknodes = list() # remember nodes that belong to hooks
for n in model.nodes():
if model.degree(n) == 1:
endnode = n
neighbour = list(model.edge[n].keys())
neighbour = neighbour[0]
add_nodes_edge_to_newmodel(model_hooks,model,n,neighbour)
hooknodes.append(neighbour)
if remove == True:
model.remove_node(n)
# Pop remaining degree 2 nodes
stentgraph.pop_nodes(model)
# Visualize
model_hooks.Draw(mc='r', mw = 10, lc='r')
# arrayn1 = np.asarray(n1)
# arrayn2 = np.asarray(n2)
# vector = np.subtract(arrayn1,arrayn2) # nodes, paths in x,y,z
# mag = np.sqrt(vector[0]**2+vector[1]**2+vector[2]**2)
# direction_x = vector[0] / mag
# direction_y = vector[1] / mag
# direction_z = vector[2] / mag
## Get Struts using direction